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, 36 (Web Server issue), W368-71

SerbGO: Searching for the Best GO Tool

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SerbGO: Searching for the Best GO Tool

J L Mosquera et al. Nucleic Acids Res.

Abstract

In recent years, the scientific community has provided many tools to assist with pathway analysis. Some of these programs can be used to manage functional annotation of gene products, others are oriented to exploring and analyzing data sets and many allow both possibilities. Potential users of these tools are faced with the necessity to decide which of the existing programs are the most appropriate for their needs. SerbGO is a user-friendly web tool created to facilitate this task. It can be used (i) to search for specific functionalities and determine which applications provide them and (ii) to compare several applications on the basis of different types of functionalities. Iterating and combining both functionalities can easily lead to selecting an appropriate tool. Data required by SerbGO is either the desired capabilities within a defined Standard Functionalities Set or the list of the tools to be compared. The analysis performed carries out a cross-classification that produces an easily readable output with the list of tools that implement the capabilities demanded or a table with the categorization of the GO tools that one wishes to compare. SerbGO is freely available and does not require a login. It can be accessed either directly at our server (http://estbioinfo.stat.ub.es/apli/serbgo) or at the GO Consortium website (http://www.geneontology.org/GO.tools.microarray.shtml#serbgo).

Figures

Figure 1.
Figure 1.
SerbGO workflow. (A) First page of the Query Form shows the Standard functionalities for the following sections: TOOL FOR, TYPE OF EXPERIMENT, INTERFACE and AVAILABILITY. (B) After the first validation a user selects the SUPPORTED SPECIES required and follows with the query until the last page. On the top-right corner is shown the number of tools available. (C) By clicking on the ‘Find’ button at the bottom of the page, the programs that fit the capabilities selected will be shown. (D) This screenshot shows the output for a list of tools and their developers. They can be compared if a user clicks on the ‘Find’ button. (E) A cross-tabulation for functionalities available in each tool is shown when the researcher requires a comparison of them. It can be attained either by comparing the output list of a Query Form or by selecting a set of tools at the Compare Tools form. (F) This page shows the entire collection of tools included in SerbGO. These programs can be compared by selecting the desired ones which query has to be validated on the button displayed at the bottom of the page.

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